kmercount/KmerCount.java
package kmercount;

import java.io.IOException;
import java.util.StringTokenizer;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.mapreduce.Mapper;
import org.apache.hadoop.mapreduce.Reducer;
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;

public class KmerCount {

    public static class TokenizerMapper
            extends Mapper<Object, Text, Text, IntWritable> {

        private final static IntWritable one = new IntWritable(1);
        private Text word = new Text();

        public void map(Object key, Text value, Context context) throws IOException, InterruptedException {
            String line = value.toString();
            if (line.contains(">gi") || line.length() < 9) {

                return;
            }

            for (int merCounter = 0; merCounter < line.length() - 9; merCounter++)

            {

                Text outputKey = new Text(line.substring(merCounter, merCounter + 9).trim());

                IntWritable outputValue = new IntWritable(1);

                context.write(outputKey, outputValue);

            }
        }
    }

    public static class IntSumReducer
            extends Reducer<Text, IntWritable, Text, IntWritable> {
        private IntWritable result = new IntWritable();

        public void reduce(Text key, Iterable<IntWritable> values,
                Context context) throws IOException, InterruptedException {
            int sum = 0;
            for (IntWritable val : values) {
                sum += val.get();
            }
            result.set(sum);
            context.write(key, result);
        }

    }

    public static void main(String[] args) throws Exception {
        Configuration conf = new Configuration();
        Job job = Job.getInstance(conf, "kmer count");
        job.setJarByClass(KmerCount.class);
        job.setMapperClass(TokenizerMapper.class);
        job.setCombinerClass(IntSumReducer.class);
        job.setReducerClass(IntSumReducer.class);
        job.setOutputKeyClass(Text.class);
        job.setOutputValueClass(IntWritable.class);
        FileInputFormat.addInputPath(job, new Path(args[0]));
        FileOutputFormat.setOutputPath(job, new Path(args[1]));
        System.exit(job.waitForCompletion(true) ? 0 : 1);
    }
}